Author: ruschein
Date: 2011-06-27 10:45:33 -0700 (Mon, 27 Jun 2011)
New Revision: 25951
Modified:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ui/ImportTablePanel.java
Log:
Enabled edge attr support.
Modified:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ui/ImportTablePanel.java
===================================================================
---
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ui/ImportTablePanel.java
2011-06-27 16:47:44 UTC (rev 25950)
+++
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ui/ImportTablePanel.java
2011-06-27 17:45:33 UTC (rev 25951)
@@ -131,23 +131,23 @@
/**
* MainUI for Table Import.
- *
+ *
* TODO: Refactor to make this more generic component.
*
*/
public class ImportTablePanel extends JPanel implements
PropertyChangeListener, TableModelListener {
private static final long serialVersionUID = 7356378931577386260L;
-
+
private static final Logger logger =
LoggerFactory.getLogger(ImportTablePanel.class);
/**
* This dialog GUI will be switched based on the following parameters:
- *
+ *
* SIMPLE_ATTRIBUTE_IMPORT: Import attributes in text table.
* ONTOLOGY_AND_ANNOTATION_IMPORT: Load ontology and map attributes in
text
* table.
- *
+ *
* NETWORK_IMPORT: Import text table as a network.
*/
public static final int SIMPLE_ATTRIBUTE_IMPORT = 1;
@@ -168,7 +168,7 @@
public static final String ATTRIBUTE_NAME_CHANGED = "aliasTableChanged";
public static final String SHEET_CHANGED = "sheetChanged";
public static final String NETWORK_IMPORT_TEMPLATE_CHANGED =
"networkImportTemplateChanged";
-
+
private static final String[] keyTable = { "Alias?", "Column (Attribute
Name)", "Data Type" };
private static final String ID = "name";
@@ -181,7 +181,7 @@
// Data Type
private
org.cytoscape.tableimport.internal.reader.TextTableReader.ObjectType objType;
private final int dialogType;
-
+
protected Map<String, String> annotationUrlMap;
protected Map<String, String> annotationFormatMap;
protected Map<String, Map<String, String>> annotationAttributesMap;
@@ -207,25 +207,25 @@
private CyTable selectedAttributes;
private PropertyChangeSupport changes = new PropertyChangeSupport(this);
private File[] inputFiles;
-
+
private CyNetwork network;
private InputStream is;
private final String fileType;
private String inputName = null;
-
+
private Workbook workbook = null;
-
+
private OntologyPanelBuilder panelBuilder;
-
+
private CyProperty<Bookmarks> bookmarksProp;
private BookmarksUtil bkUtil;
-
+
private final InputStreamTaskFactory factory;
private final TaskManager taskManager;
-
+
private final CyNetworkManager manager;
-
+
private final CyTableFactory tableFactory;
public ImportTablePanel(int dialogType, final InputStream is, String
fileType, String inputName,
@@ -236,7 +236,7 @@
this(dialogType, is, fileType, bookmarksProp, bkUtil,
taskManager, factory, manager, tableFactory);
this.inputName = inputName;
}
-
+
public ImportTablePanel(int dialogType, final InputStream is, String
fileType,
final CyProperty<Bookmarks> bookmarksProp, final
BookmarksUtil bkUtil, final TaskManager taskManager,
final InputStreamTaskFactory factory, final
CyNetworkManager manager, final CyTableFactory tableFactory)
@@ -246,7 +246,7 @@
this.factory = factory;
this.manager = manager;
this.tableFactory = tableFactory;
-
+
if (dialogType == ONTOLOGY_AND_ANNOTATION_IMPORT) {
if (bookmarksProp == null)
throw new NullPointerException("Bookmark
Property is null.");
@@ -255,15 +255,15 @@
this.bookmarksProp = bookmarksProp;
this.bkUtil = bkUtil;
-
+
}
this.is = is;
this.fileType = fileType;
selectedAttributes = null;
-
+
network = CytoscapeServices.appMgr.getCurrentNetwork();
if (network != null){
- selectedAttributes =
CytoscapeServices.tblMgr.getTableMap(CyNode.class,
network).get(CyNetwork.DEFAULT_ATTRS);
+ selectedAttributes =
CytoscapeServices.tblMgr.getTableMap(CyNode.class,
network).get(CyNetwork.DEFAULT_ATTRS);
}
this.objType = NODE;
this.dialogType = dialogType;
@@ -284,23 +284,23 @@
attributeDataTypes = new ArrayList<Byte>();
initComponents();
-
+
// Hide two unwanted button
this.importButton.setVisible(false);
- this.cancelButton.setVisible(false);
-
+ this.cancelButton.setVisible(false);
+
updateComponents();
previewPanel.addPropertyChangeListener(this);
-
+
//Don't know why this panel is disabled at start up
this.attributeNamePanel.setEnabled(true);
-
+
// Hide input file and use inputStream
this.attributeFileLabel.setVisible(false);
this.selectAttributeFileButton.setVisible(false);
this.targetDataSourceTextField.setVisible(false);
-
+
//Case import network
if (this.dialogType == NETWORK_IMPORT) {
this.edgeRadioButton.setVisible(false);
@@ -308,18 +308,15 @@
}
// Case import node/edge attribute
- if (this.dialogType == SIMPLE_ATTRIBUTE_IMPORT) {
+ if (this.dialogType == SIMPLE_ATTRIBUTE_IMPORT)
this.networkRadioButton.setVisible(false);
- // we will handle edge attribute import late
- this.edgeRadioButton.setVisible(false);
- }
-
+
this.helpButton.setVisible(false);
-
+
setPreviewPanel(null);
}
-
-
+
+
public void addPropertyChangeListener(PropertyChangeListener l) {
if(changes == null) return;
changes.addPropertyChangeListener(l);
@@ -646,7 +643,7 @@
.add(attribuiteLabel).add(nodeRadioButton).add(edgeRadioButton).add(networkRadioButton)));
}
-
+
if (dialogType == ONTOLOGY_AND_ANNOTATION_IMPORT) {
panelBuilder = new OntologyPanelBuilder(this,
bookmarksProp, bkUtil, taskManager, factory, manager, tableFactory);
panelBuilder.buildPanel();
@@ -663,7 +660,7 @@
try {
setPreviewPanel(evt);
} catch (IOException e) {
-
+
JOptionPane.showMessageDialog(ImportTablePanel.this, "<html>Could not read
selected file.<p>See <b>Help->Error Dialog</b> for further details.</html>",
"ERROR", JOptionPane.ERROR_MESSAGE);
logger.warn("Could not
read selected file.", e);
}
@@ -1251,7 +1248,7 @@
// Update primary key index.
keyInFile = primaryKeyComboBox.getSelectedIndex();
- // Update
+ // Update
previewPanel.getPreviewTable()
.setDefaultRenderer(Object.class,
getRenderer(previewPanel.getFileType()));
@@ -1299,20 +1296,20 @@
private void attributeRadioButtonActionPerformed(ActionEvent evt) {
CyNetwork network =
CytoscapeServices.appMgr.getCurrentNetwork();
-
+
if (nodeRadioButton.isSelected()) {
//selectedAttributes = Cytoscape.getNodeAttributes();
if (network != null){
- selectedAttributes =
CytoscapeServices.tblMgr.getTableMap(CyNode.class,
network).get(CyNetwork.DEFAULT_ATTRS);
+ selectedAttributes =
CytoscapeServices.tblMgr.getTableMap(CyNode.class,
network).get(CyNetwork.DEFAULT_ATTRS);
}
-
+
objType = NODE;
} else if (edgeRadioButton.isSelected()) {
//selectedAttributes = Cytoscape.getEdgeAttributes();
if (network != null){
- selectedAttributes =
CytoscapeServices.tblMgr.getTableMap(CyEdge.class,
network).get(CyNetwork.DEFAULT_ATTRS);
+ selectedAttributes =
CytoscapeServices.tblMgr.getTableMap(CyEdge.class,
network).get(CyNetwork.DEFAULT_ATTRS);
}
-
+
objType = EDGE;
} else {
//selectedAttributes = Cytoscape.getNetworkAttributes();
@@ -1339,7 +1336,7 @@
JDialog dlg =
(JDialog)this.getParent().getParent().getParent().getParent().getParent().getParent();
dlg.pack();
-
+
//pack();
}
@@ -1364,8 +1361,8 @@
setKeyList();
}
-
+
private void
transferNameCheckBoxActionPerformed(java.awt.event.ActionEvent evt) {
final DefaultTableModel model = (DefaultTableModel)
previewPanel.getPreviewTable().getModel();
@@ -1416,7 +1413,7 @@
repaint();
}
-
+
/**
* Load from the data source.<br>
*
@@ -1426,7 +1423,7 @@
public void importTable() throws Exception {
if (checkDataSourceError() == false)
return;
-
+
boolean importAll = importAllCheckBox.isSelected();
/*
@@ -1499,7 +1496,7 @@
//final byte[] attributeTypes = new
byte[previewPanel.getPreviewTable()
// .getColumnCount()];
final Byte[] test =
previewPanel.getDataTypes(previewPanel.getSelectedSheetName());
-
+
final Byte[] attributeTypes = new Byte[test.length];
for (int i = 0; i < test.length; i++) {
@@ -1547,10 +1544,10 @@
switch (dialogType) {
case SIMPLE_ATTRIBUTE_IMPORT:
// Case 1: Attribute table import.
-
+
// Extract URL from the text table.
//final URL source = new
URL(targetDataSourceTextField.getText());
-
+
// Make sure primary key index is up-to-date.
keyInFile =
primaryKeyComboBox.getSelectedIndex();
@@ -1566,40 +1563,38 @@
del = checkDelimiter();
//}
- //TODO -- Need to fix problem in
AttributeMappingParameters
+ //TODO -- Need to fix problem in
AttributeMappingParameters
mapping = new
AttributeMappingParameters(objType, del,
-
listDelimiter, keyInFile,
-
mappingAttribute, aliasList,
-
attributeNames, attributeTypes,
-
listDataTypes, importFlag,
-
caseSensitive);
-
- //if
(source.toString().endsWith(SupportedFileType.EXCEL.getExtension()) ||
+
listDelimiter, keyInFile,
+
mappingAttribute, aliasList,
+
attributeNames, attributeTypes,
+
listDataTypes, importFlag,
+
caseSensitive);
+
+ //if
(source.toString().endsWith(SupportedFileType.EXCEL.getExtension()) ||
//
source.toString().endsWith(SupportedFileType.OOXML.getExtension())) {
- if
(this.fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension()) ||
-
this.fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) {
+ if
(this.fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension()) ||
+
this.fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension()))
+ {
+ if (workbook == null)
+ throw new
NullPointerException("Wookbook object is null!");
- if(workbook == null)
- throw new
NullPointerException("Wrokbook object is null.");
-
// Load all sheets in the table
for (int i = 0; i <
workbook.getNumberOfSheets(); i++) {
final Sheet sheet =
workbook.getSheetAt(i);
loadAnnotation(new
ExcelAttributeSheetReader(sheet, mapping,
startLineNumber,
-
importAll),
-
null);
-
//source.toString());
+
importAll),
+ null);
+ //source.toString());
}
} else {
loadAnnotation(new
DefaultAttributeTableReader(null, mapping,
-
startLineNumber,
-
null, importAll, this.is),
-
null);
-
//source.toString());
+
startLineNumber,
+
null, importAll, this.is),
+ null);
}
-
break;
case ONTOLOGY_AND_ANNOTATION_IMPORT:
@@ -1622,7 +1617,7 @@
//}
//final URL networkSource = new
URL(targetDataSourceTextField.getText());
-
+
final int sourceColumnIndex =
networkImportPanel.getSourceIndex();
final int targetColumnIndex =
networkImportPanel.getTargetIndex();
@@ -1645,81 +1640,44 @@
//boolean multi = false;
//System.out.println("ImportTablePanel.importTable(): sources.length ="+
sources.length);
-
+
//if (sources.length == 1)
//multi = false;
//for (int i = 0; i < sources.length; i++) {
// if
(sources[i].toString().endsWith(SupportedFileType.EXCEL.getExtension()) ||
sources[i].toString().endsWith(SupportedFileType.OOXML.getExtension())) {
-
- if
(this.fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension()) ||
-
this.fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) {
- // Extract name from the sheet
name.
- //InputStream is = null;
- //Workbook wb = null;
- //try {
- //is =
sources[i].openStream();
-
- //wb =
WorkbookFactory.create(is);
- //}
- //catch (Exception e){
- // e.printStackTrace();
- //}
- //finally {
- // if (is != null) {
- // is.close();
- // }
- //}
-
- Sheet sheet =
workbook.getSheetAt(0);
- networkName =
workbook.getSheetName(0);
-
- reader = new
ExcelNetworkSheetReader(networkName, sheet, nmp,
+ if
(this.fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension()) ||
+
this.fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension()))
+ {
+ Sheet sheet = workbook.getSheetAt(0);
+ networkName = workbook.getSheetName(0);
+
+ reader = new
ExcelNetworkSheetReader(networkName, sheet, nmp,
startLineNumber);
- } else {
- // Get name from URL.
- if ((commentChar != null) &&
(commentChar.length() != 0)
- &&
transferNameCheckBox.isSelected()) {
- startLineNumber++;
- }
-
- //final String[] parts =
sources[i].toString().split("/");
- //networkName =
parts[parts.length - 1];
- networkName = this.inputName;
-
-
- reader = new
NetworkTableReader(networkName, this.is, nmp,
-
startLineNumber, commentChar);
- }
- loadNetwork(reader);
- //}
+ } else {
+ // Get name from URL.
+ if ((commentChar != null) &&
(commentChar.length() != 0)
+ &&
transferNameCheckBox.isSelected())
+ startLineNumber++;
- //if (multi) {
- //StringBuilder builder = new
StringBuilder();
- //builder.append("The following
networks are loaded:\n\n");
-
- //for (File f : inputFiles) {
- //builder.append(f.getName() +
"\n");
- //}
-
- //JOptionPane.showMessageDialog(this,
builder.toString(),
- //
"Multiple Networks Loaded",
- //
JOptionPane.INFORMATION_MESSAGE);
- //}
-
+ networkName = this.inputName;
+ reader = new
NetworkTableReader(networkName, this.is, nmp,
+
startLineNumber, commentChar);
+ }
+ loadNetwork(reader);
break;
default:
return;
}
}
-
+
private void setPreviewPanel(ActionEvent evt) throws IOException {
/*
final File[] multiSource =
CytoscapeServices.fileUtil.getFiles(this,
- "Select local file",
+ "Select local file",
CytoscapeServices.fileUtil.LOAD);
if ((multiSource == null) || (multiSource[0] == null))
@@ -1749,7 +1707,7 @@
readAnnotationForPreview(null, checkDelimiter());
transferNameCheckBox.setEnabled(true);
transferNameCheckBox.setSelected(false);
-
+
if (previewPanel.getPreviewTable() == null) {
// JLabel label = new JLabel("File is broken or empty!");
// label.setForeground(Color.RED);
@@ -1777,7 +1735,7 @@
//((JDialog)this.getParent().getParent().getParent().getParent().getParent().getParent()).pack();
}
-
+
private void reloadButtonActionPerformed(java.awt.event.ActionEvent evt)
throws IOException {
displayPreview();
@@ -1844,7 +1802,7 @@
return aliasList;
}
-
+
private void displayPreview() throws IOException {
final String selectedSourceName;
//final URL sourceURL;
@@ -1862,7 +1820,7 @@
}
private void updateComponents() throws JAXBException, IOException {
-
+
if (dialogType == SIMPLE_ATTRIBUTE_IMPORT) {
//setTitle("Import Annotation File");
titleLabel.setText("Import Attribute from Table");
@@ -1872,7 +1830,7 @@
//setTitle("Import Ontology Data and Annotations");
titleLabel.setText("Import Ontology and Annotation");
ontology2annotationPanel.setVisible(false);
-
+
// Update available file lists.
panelBuilder.setOntologyComboBox();
panelBuilder.setAnnotationComboBox();
@@ -1898,7 +1856,7 @@
// do nothing
}
else { // attribute import
- updateMappingAttributeComboBox();
+ updateMappingAttributeComboBox();
}
setStatusBar("-", "-", "File Size: Unknown");
@@ -1984,7 +1942,7 @@
private void setOntologyInAnnotationComboBox() {
final DefaultTableModel model = (DefaultTableModel)
previewPanel.getPreviewTable().getModel();
-
+
if ((model != null) && (model.getColumnCount() > 0)) {
ontologyInAnnotationComboBox.removeAllItems();
@@ -1998,18 +1956,18 @@
ontologyInAnnotationComboBox.setEnabled(true);
}
-
+
/**
* Display preview table
- *
+ *
* @param sourceURL
* @param delimiters
* @throws IOException
*/
protected void readAnnotationForPreview(URL sourceURL, List<String>
delimiters) throws IOException {
-
+
/*
* Check number of lines we should load. if -1, load everything
in the
* file.
@@ -2026,7 +1984,7 @@
*/
final String commentChar = commentLineTextField.getText();
final int startLine =
Integer.parseInt(startRowSpinner.getValue().toString());
-
+
// Load Spreadsheet data for preview.
if(fileType != null && (fileType.equalsIgnoreCase(
SupportedFileType.EXCEL.getExtension())
@@ -2056,11 +2014,11 @@
if (!is_isClosed){
this.is.mark(Integer.MAX_VALUE);
}
-
+
previewPanel.setPreviewTable(workbook, this.is, this.fileType,
sourceURL, delimiters, null, previewSize,
commentChar, startLine - 1);
-
+
// Reset the inputStream to the mark after preview
if (!is_isClosed){
this.is.reset();
@@ -2079,7 +2037,7 @@
listDataTypes = previewPanel.getCurrentListDataTypes();
-
+
if (dialogType == NETWORK_IMPORT) {
final String[] columnNames = new
String[previewPanel.getPreviewTable().getColumnCount()];
@@ -2087,8 +2045,8 @@
columnNames[i] =
previewPanel.getPreviewTable().getColumnName(i);
networkImportPanel.setComboBoxes(columnNames);
-
- if
(this.fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension()) ||
+
+ if
(this.fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension()) ||
this.fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) {
switchDelimiterCheckBoxes(false);
} else {
@@ -2101,10 +2059,10 @@
rend.setSourceIndex(AttributePreviewTableCellRenderer.PARAMETER_NOT_EXIST);
rend.setTargetIndex(AttributePreviewTableCellRenderer.PARAMETER_NOT_EXIST);
rend.setInteractionIndex(AttributePreviewTableCellRenderer.PARAMETER_NOT_EXIST);
- } else {
+ } else {
for (int i = 0; i < previewPanel.getTableCount(); i++) {
final int columnCount =
previewPanel.getPreviewTable(i).getColumnCount();
-
+
aliasTableModelMap.put(previewPanel.getSheetName(i),
new
AliasTableModel(keyTable, columnCount));
@@ -2127,7 +2085,7 @@
updatePrimaryKeyComboBox();
}
-
+
setOntologyInAnnotationComboBox();
/*
* If this is not an Excel file, enable delimiter
checkboxes.
@@ -2157,7 +2115,7 @@
*/
//setStatusBar(sourceURL);
}
-
+
reloadButton.setEnabled(true);
startRowSpinner.setEnabled(true);
startRowLabel.setEnabled(true);
@@ -2199,13 +2157,13 @@
private FileTypes checkFileType(URL source) {
//String[] parts = source.toString().split("/");
-
+
//final String fileName = parts[parts.length - 1];
//if (fileName.startsWith("gene_association")
// && (dialogType == ONTOLOGY_AND_ANNOTATION_IMPORT)) {
// return FileTypes.GENE_ASSOCIATION_FILE;
- //} else
+ //} else
if (dialogType == ONTOLOGY_AND_ANNOTATION_IMPORT) {
return FileTypes.CUSTOM_ANNOTATION_FILE;
} else if (dialogType == NETWORK_IMPORT) {
@@ -2261,9 +2219,9 @@
}
if (CytoscapeServices.appMgr.getCurrentNetwork() == null){
- return;
+ return;
}
-
+
String selectedKeyAttribute =
mappingAttributeComboBox.getSelectedItem().toString();
Iterator it;
@@ -2272,7 +2230,7 @@
//TODO -- setKeyList
if (selectedKeyAttribute.equals(ID)) {
-
+
if (objType == NODE) {
//it = Cytoscape.getRootGraph().nodesIterator();
it = network.getNodeList().iterator();
@@ -2294,11 +2252,11 @@
//}
}
} else {
-
+
//TODO
/*
final byte attrType =
selectedAttributes.getType(selectedKeyAttribute);
-
+
Object value = null;
Iterator attrIt = selectedAttributes.getMultiHashMap()
@@ -2310,17 +2268,17 @@
Boolean boolValue = false;
List listValue = null;
-
+
while (attrIt.hasNext()) {
value = attrIt.next();
-
+
switch (attrType) {
case AttributeTypes.TYPE_STRING:
//stringValue =
selectedAttributes.getStringAttribute((String) value,
//
selectedKeyAttribute);
stringValue =
selectedAttributes.getColumnValues(selectedKeyAttribute, String.class);
-
+
valueSet.add(stringValue);
break;
@@ -2356,7 +2314,7 @@
default:
break;
}
-
+
}
*/
}
@@ -2483,7 +2441,7 @@
}
private void updateMappingAttributeComboBox() {
-
+
mappingAttributeComboBox.removeAllItems();
final ListCellRenderer lcr =
mappingAttributeComboBox.getRenderer();
@@ -2508,13 +2466,13 @@
if (CytoscapeServices.appMgr.getCurrentNetwork() == null)
return;
-
+
for (final CyColumn column : selectedAttributes.getColumns()) {
final String columnName = column.getName();
if (columnName.equalsIgnoreCase(ID))
continue;
-
- final Class<?> type = column.getType();
+
+ final Class<?> type = column.getType();
if (type == String.class || type == Integer.class ||
type == Double.class || type == List.class)
mappingAttributeComboBox.addItem(columnName);
}
@@ -2560,16 +2518,16 @@
* @param source
*/
private void loadAnnotation(TextTableReader reader, String source) {
-
+
// Create loadAnnotation Task
- final ImportAttributeTableTaskFactory factory = new
ImportAttributeTableTaskFactory(reader);
+ final ImportAttributeTableTaskFactory factory = new
ImportAttributeTableTaskFactory(reader);
this.loadTask = factory.getTaskIterator().next();
//ImportAttributeTableTaskFactory taskFactory = new
ImportAttributeTableTaskFactory(task);
//CytoscapeServices.guiTaskManagerServiceRef.execute(taskFactory);
}
private Task loadTask = null;
-
+
public Task getLoadTask(){
return loadTask;
}
@@ -2582,7 +2540,7 @@
//ImportNetworkTaskFactory taskFactory = new
ImportNetworkTaskFactory(task);
//CytoscapeServices.guiTaskManagerServiceRef.execute(taskFactory);
}
-
+
private void setStatusBar(String message1, String message2, String
message3) {
statusBar.setLeftLabel(message1);
statusBar.setCenterLabel(message2);
@@ -2862,7 +2820,7 @@
annotationAndOntologyImportPanel.setVisible(true);
attrTypePanel.setVisible(true);
} else if (dialogType == NETWORK_IMPORT) {
-
+
layout.setHorizontalGroup(layout.createParallelGroup(GroupLayout.LEADING).add(
layout.createSequentialGroup()
.addContainerGap()
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